Merge pull request #8 from Remi-Gau/dev

make it easy to adapt stimuli to the screen dimension

Author: Remi-Gau

.github/workflows/moxunit.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+    - name: MOxUnit Action
+      uses: joergbrech/moxunit-action@v1.1
+      with:
+        tests: tests
+        src: subfun
+        with_coverage: true
+        cover_xml_file: coverage.xml
+    - name: Code coverage
+      uses: codecov/codecov-action@v1
+      with:
+       token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+       file:  coverage.xml # optional
+       flags: unittests # optional
+       name: codecov-umbrella # optional
+       fail_ci_if_error: true # optional (default = false)

README.md

@@ -1,36 +1,59 @@
+[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_retinotopy/actions)
+![](https://github.com/cpp-lln-lab/CPP_retinotopy/workflows/CI/badge.svg)
+
+[![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_retinotopy/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_retinotopy)
+
+[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_retinotopy.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_retinotopy)
+
 # RETINOTOPIC MAPPING STIMULUS
 
+<!-- vscode-markdown-toc -->
+
+- 1. [Depdendencies](#Depdendencies) \* 1.1. [mpm (beta)](#mpmbeta)
+- 2. [Running the experiment](#Runningtheexperiment)
+     _ 2.1. [Set up](#Setup)
+     _ 2.2. [Running the retinotopy scripts](#Runningtheretinotopyscripts)
+- 3. [Other scripts](#Otherscripts)
+- 4. [Reporting a problem](#Reportingaproblem)
+- 5. [Contributors](#Contributors)
+
+<!-- vscode-markdown-toc-config
+	numbering=true
+	autoSave=true
+	/vscode-markdown-toc-config -->
+<!-- /vscode-markdown-toc -->
 
-## Depdendencies
+## 1. <a name='Depdendencies'></a>Depdendencies
 
 | Dependencies                                             | Used version |
-|----------------------------------------------------------|--------------|
+| -------------------------------------------------------- | ------------ |
 | [Matlab](https://www.mathworks.com/products/matlab.html) | 20???        |
 | or [Octave](https://www.gnu.org/software/octave/)        | 4.?          |
-| [Psychtoolbox](http://psychtoolbox.org/)                 | v3.15         |
-| [JSONio](https://github.com/gllmflndn/JSONio)                 | NA         |
+| [Psychtoolbox](http://psychtoolbox.org/)                 | v3.15        |
+| [JSONio](https://github.com/gllmflndn/JSONio)            | NA           |
 
-### mpm (beta)
+### 1.1. <a name='mpmbeta'></a>mpm (beta)
 
 You can use [matlab package manager](https://github.com/mobeets/mpm) to install the dependencies.
 
 ```matlab
 mpm install -i fullpath_to_this_folder/dependencies.txt -c PTB_retinotopy --allpaths
 ```
 
-## Running the experiment
+## 2. <a name='Runningtheexperiment'></a>Running the experiment
 
-### Set up
+### 2.1. <a name='Setup'></a>Set up
 
 Before you can begin you will need to generate a checkerboard or ripple stimulus with the dimensions of the screen you are using for your experiment. For this, you will need to modify the script `GenCheckerboard.m` or `GenRipples.m` in the `input` folder and change the variable `width` or the `height` of your screen in pixels. After running this script the new checkerboard stimulus will be saved on your disk.
 
 Some other things will need to be changed to match your needs. Most of it should be in :
 
 - `SetParameters.m`
-  - The parameter `Resolution` needs to be changed to reflect your screen dimensions (e.g. `[0 0 1024 768]` for 1024*768).
+  - The parameter `Resolution` needs to be changed to reflect your screen dimensions (e.g. `[0 0 1024 768]` for 1024\*768).
   - The parameters `TR` and `Dummies` need to be adjusted for your scanner sequence.
 
 In the following
+
 - `Polar.m`
 - `Eccen.m`
 - `DriftingBar`
@@ -39,27 +62,25 @@ you will need to adapt the `VolsPerCycle` parameter such that you have enough vo
 
 For example, if your TR is 2 seconds you would want to have 30 volumes per cycle. (Note that shorter cycles work as well, but for inexperienced participants a minute per cycle is probably optimal).
 
-### Running the retinotopy scripts
+### 2.2. <a name='Runningtheretinotopyscripts'></a>Running the retinotopy scripts
 
 Any of the other parameters probably do not need to be changed at all.
 
 Calling the `Polar` and `Eccen` program without any input arguments will run a demo which is triggered manually by pressing a key.
 
 The first input argument is the subject name/ID, the second (optional) input argument defines the direction the stimulus is moving (that is either clockwise vs anticlockwise or contracting vs expanding).
 
-
-## Other scripts
+## 3. <a name='Otherscripts'></a>Other scripts
 
 There are also two scripts which can be used for population receptive field mapping. One is the standard protocol with bars traversing the visual field as in Dumoulin & Wandell (2008).
 
 In addition, there is a dual phase-encoded protocol with which you could theoretically map both the polar angle and the eccentricity in the same scan. By including blank periods this could also be used in order to map population receptive fields. This still needs refactoring.
 
-
-## Reporting a problem
+## 4. <a name='Reportingaproblem'></a>Reporting a problem
 
 Get in touch by reporting an issue or sending a pull request
 
-## Contributors
+## 5. <a name='Contributors'></a>Contributors
 
 Original version by [Sam Schwarzkopf](https://sampendu.net/sam-schwarzkopf/) (27th July 2010)
 
@@ -68,7 +89,7 @@ Some modifications (esp for eye tracking) have been done by [Tim Rohe](https://s
 Code cleaning and refactoring was done by Rémi Gau.
 
 The loose style guide used here:
+
 - use `PascalCase`
 - structures that are passed around and centralize a lot of information (TARGET, BEHAVIOUR, PARAMETERS...) are in upper case
 - [McCabe complexity](https://en.wikipedia.org/wiki/Cyclomatic_complexity) has to be inferior to 15 (see `checkcode('foo.m', '-cyc')`)
-

driftingBars.m

@@ -5,62 +5,62 @@ function driftingBars(debug, stim, emul)
     %   Subj :  String with subject ID
     %   Stim :  Stimulus file name e.g. 'Checkerboard'
     %   Emul :  0 = Triggered by scanner, 1 = Trigger by keypress
-    
+
     if nargin < 1 || isempty(debug)
         debug = 1;
     end
     if nargin < 2  || isempty(stim)
         stim = 'Ripples.mat';
     end
     if nargin < 3  || isempty(emul)
-        emul = 1;
+        emul = 0;
     end
 
     initEnv();
-    
+
     %% Experimental Parameters
-    
+
     cfg.task.name = 'retinotopy drifting bar';
-    
+
     % Stimulus type
     cfg.aperture.type = 'bar';
-    
+
     % Stimulus conditions in each block defined by number
-    cfg.conditions = [90 45 0 135 270 225 180 315];
-    
+    cfg.conditions = [90 45 135 270 225 315 90 45 135 270 225 315];
+
     %% Set defaults
-    
+
     cfg.stim = stim;
     cfg.debug.do = debug;
-    
+
     if ~emul
         cfg.testingDevice = 'mri';
     else
         cfg.testingDevice = 'pc';
     end
-    
+
     cfg.extraColumns.bar_angle = struct( ...
         'length', 1, ...
         'bids', struct( ...
         'LongName', 'bar angle', ...
         'Description', '', ...
         'Units', 'degrees'));
-    
+
     cfg.extraColumns.bar_width = struct( ...
         'length', 1, ...
         'bids', struct( ...
         'LongName', 'width of the bar', ...
         'Description', '', ...
         'Units', 'degrees'));
-    
+
     cfg.extraColumns.bar_position = struct( ...
         'length', 1, ...
         'bids', struct( ...
         'LongName', '', ...
         'Description', 'bar position with respoect to the fixation cross', ...
         'Units', 'degrees'));
-    
+
     [cfg] = setParameters(cfg);
-    
+
     %% Run the experiment
     barsMapping(cfg);

initEnv.m

@@ -8,14 +8,16 @@
 %       - struct
 %       - statistics
 %
-%   MATLAB > R2017a
+%   MATLAB >= R2015b
 %
 % 2 - Add project to the O/M path
 
 function initEnv
 
     octaveVersion = '4.0.3';
-    matlabVersion = '9.2.0';
+    matlabVersion = '8.6.0';
+
+    installlist = {'io', 'statistics', 'image'};
 
     if isOctave
 
@@ -24,27 +26,19 @@
             error('Minimum required Octave version: %s', octaveVersion);
         end
 
-        installlist = {'statistics'};
         for ii = 1:length(installlist)
+
+            packageName = installlist{ii};
+
             try
                 % Try loading Octave packages
-                disp(['loading ' installlist{ii}]);
-                pkg('load', installlist{ii});
+                disp(['loading ' packageName]);
+                pkg('load', packageName);
 
             catch
-                errorcount = 1;
-                while errorcount % Attempt twice in case installation fails
-                    try
-                        pkg('install', '-forge', installlist{ii});
-                        pkg('load', installlist{ii});
-                        errorcount = 0;
-                    catch err
-                        errorcount = errorcount + 1;
-                        if errorcount > 2
-                            error(err.message);
-                        end
-                    end
-                end
+
+                tryInstallFromForge(packageName);
+
             end
         end
 
@@ -58,7 +52,9 @@
 
     % If external dir is empty throw an exception
     % and ask user to update submodules.
-    if numel(dir('lib')) <= 2 % Means that the external is empty
+    libDirectory = fullfile(fileparts(mfilename('fullpath')), 'lib');
+
+    if numel(dir(libDirectory)) <= 2 % Means that the external is empty
         error(['Git submodules are not cloned!', ...
               'Try this in your terminal:', ...
               ' git submodule update --recursive ']);
@@ -70,25 +66,41 @@
 
 end
 
-%%
-%% Return: true if the environment is Octave.
-%%
 function retval = isOctave
+    % Return: true if the environment is Octave.
     persistent cacheval   % speeds up repeated calls
 
     if isempty (cacheval)
-        cacheval = (exist ("OCTAVE_VERSION", "builtin") > 0);
+        cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
     end
 
     retval = cacheval;
+
+end
+
+function tryInstallFromForge(packageName)
+
+    errorcount = 1;
+    while errorcount % Attempt twice in case installation fails
+        try
+            pkg('install', '-forge', packageName);
+            pkg('load', packageName);
+            errorcount = 0;
+        catch err
+            errorcount = errorcount + 1;
+            if errorcount > 2
+                error(err.message);
+            end
+        end
+    end
+
 end
 
 function addDependencies()
 
     pth = fileparts(mfilename('fullpath'));
-    addpath(fullfile(pth, 'lib', 'CPP_BIDS', 'src'));
-    addpath(fullfile(pth, 'lib', 'CPP_PTB', 'src', 'aperture'));
-    addpath(fullfile(pth, 'lib', 'CPP_PTB'));
+    addpath(genpath(fullfile(pth, 'lib', 'CPP_BIDS', 'src')));
+    addpath(genpath(fullfile(pth, 'lib', 'CPP_PTB', 'src')));
     addpath(genpath(fullfile(pth, 'subfun')));
 
 end

input/genRipples.m

@@ -1,6 +1,6 @@
 % Define here the height of the screen minus a few pixels
 
-Height = 1080;
+Height = 1000;
 
 Phases = 0:10:355;
 

lib/CPP_BIDS

@@ -1,4 +1,10 @@
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
-suppress_rule: "copyright_notice"
-exclude_dir: "lib"
 regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
+suppress_rule: "copyright_notice"
+
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 15
+metric "parameters": limit 5

lib/CPP_PTB

@@ -10,7 +10,7 @@
 
     ringSpeed = widthFOV ./ cycleDur;
     stayRingSec =  widthRing ./ ringSpeed; % time ring needs to pass a voxel
-    stickFct = mod(time, cycleDur) < stayRingSec ;
+    stickFct = mod(time, cycleDur) < stayRingSec;
     [hrf, p] = spm_hrf(TR);
     Y = filter(hrf', 1, stickFct);
     Y = Y + randn(length(timeSpan), length(widthRingRange), length(cycleDurRange));
@@ -20,7 +20,7 @@
                 cos(time(:, iWidth, iCycle) * 2 * pi / cycleDur(1, iWidth, iCycle)), ...
                 ones(length(timeSpan), 1)];
             [param, dev, stats] = glmfit(X, Y(:, iWidth, iCycle), 'normal');
-            ResVar = dev * 1 / (length(timeSpan) - 3) ;
+            ResVar = dev * 1 / (length(timeSpan) - 3);
             F(iWidth, iCycle) = (sum(param(1:2).^2) / 3) / ResVar;
             power(iWidth, iCycle) = abs(param(2) + i * param(1));
         end